Remove incorrect references to rds

Since we (mostly) don't use rds anymore these references are incorrect and potentially confusing.

I've updated lots of documentation to remove the reference to rds.

I've also updated many comments that mentioned rds (these were probably the most confusing).

R/process_costs_rmd.R

@@ -14,7 +14,8 @@ process_costs_rmd <- function(file_name) {
     stringr::fixed("Rmd", ignore_case = TRUE)
   )) {
     cli::cli_abort(
-      "{.arg file_name} must be an {.code .Rmd} not a {.code .{fs::path_ext(file_name)}}."
+      "{.arg file_name} must be an {.code .Rmd} not a
+      {.code .{fs::path_ext(file_name)}}."
     )
   }
 
@@ -34,7 +35,12 @@ process_costs_rmd <- function(file_name) {
 
   output_file <- get_file_path(
     directory = output_dir,
-    file_name = fs::path_ext_set(stringr::str_glue("{fs::path_ext_remove(file_name)}-{latest_update()}-{date_today}"), "html"),
+    file_name = fs::path_ext_set(
+      stringr::str_glue(
+        "{fs::path_ext_remove(file_name)}-{latest_update()}-{date_today}"
+      ),
+      "html"
+    ),
     check_mode = "write"
   )
 
@@ -55,7 +61,7 @@ process_costs_rmd <- function(file_name) {
 #'
 #' @description This will read and process the
 #' District Nursing cost lookup, it will return the final data
-#' but also write this out as a rds.
+#' and write it to disk.
 #'
 #' @param file_path Path to the cost lookup.
 #'
@@ -73,7 +79,7 @@ process_costs_dn_rmd <- function(file_path = get_dn_costs_path()) {
 #'
 #' @description This will read and process the
 #' care homes cost lookup, it will return the final data
-#' but also write this out as a rds.
+#' and write it to disk.
 #'
 #' @inheritParams process_costs_dn_rmd
 #'
@@ -91,7 +97,7 @@ process_costs_ch_rmd <- function(file_path = get_ch_costs_path()) {
 #'
 #' @description This will read and process the
 #' GP ooh cost lookup, it will return the final data
-#' but also write this out as a rds.
+#' and write it to disk.
 #'
 #' @inheritParams process_costs_dn_rmd
 #'
@@ -109,7 +115,7 @@ process_costs_gp_ooh_rmd <- function(file_path = get_gp_ooh_costs_path()) {
 #'
 #' @description This will read and process the
 #' Home Care cost lookup, it will return the final data
-#' but also write this out as a rds.
+#' and write it to disk.
 #'
 #' @inheritParams process_costs_dn_rmd
 #'

R/process_extract_acute.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' acute extract, it will return the final data
-#' but also write this out as an rds.
+#' and (optionally) write it to disk.
 #'
 #' @param data The extract to process
 #' @param year The year to process, in FY format.
@@ -61,9 +61,7 @@ process_extract_acute <- function(data, year, write_to_disk = TRUE) {
       levels = 0L:8L
     ))
 
-
-  ## save outfile ---------------------------------------
-  outfile <- acute_clean %>%
+  acute_processed <- acute_clean %>%
     dplyr::select(
       "year",
       "recid",
@@ -113,10 +111,11 @@ process_extract_acute <- function(data, year, write_to_disk = TRUE) {
     dplyr::arrange(.data$chi, .data$record_keydate1)
 
   if (write_to_disk) {
-    # Save as rds file
-    outfile %>%
-      write_file(get_source_extract_path(year, "Acute", check_mode = "write"))
+    write_file(
+      acute_processed,
+      get_source_extract_path(year, "Acute", check_mode = "write")
+    )
   }
 
-  return(outfile)
+  return(acute_processed)
 }

R/process_extract_ae.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' A&E extract, it will return the final data
-#' but also write this out as an rds.
+#' and (optionally) write it to disk.
 #'
 #' @param data The extract to process
 #' @param year The year to process, in FY format.
@@ -237,9 +237,7 @@ process_extract_ae <- function(data, year, write_to_disk = TRUE) {
       .data$keytime2
     )
 
-
-  # Save outfile----------------------------------------
-  outfile <- matched_ae_data %>%
+  ae_processed <- matched_ae_data %>%
     dplyr::select(
       "year",
       "recid",
@@ -294,10 +292,11 @@ process_extract_ae <- function(data, year, write_to_disk = TRUE) {
     )
 
   if (write_to_disk) {
-    # Save as rds file
-    outfile %>%
-      write_file(get_source_extract_path(year, "AE", check_mode = "write"))
+    write_file(
+      ae_processed,
+      get_source_extract_path(year, "AE", check_mode = "write")
+    )
   }
 
-  return(outfile)
+  return(ae_processed)
 }

R/process_extract_alarms_telecare.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' (year specific) Alarms Telecare extract, it will return the final data
-#' but also write this out as rds.
+#' and (optionally) write it to disk.
 #'
 #' @inheritParams process_extract_care_home
 #'

R/process_extract_care_home.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' (year specific) Care Home extract, it will return the final data
-#' but also write this out as rds.
+#' and (optionally) write it to disk.
 #'
 #' @param data The full processed data which will be selected from to create
 #' the year specific data.

R/process_extract_cmh.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' CMH extract, it will return the final data
-#' but also write this out as an rds.
+#' and (optionally) write it to disk.
 #'
 #' @param data The extract to process
 #' @param year The year to process, in FY format.
@@ -44,9 +44,7 @@ process_extract_cmh <- function(data,
     # create blank diag 6
     dplyr::mutate(diag6 = NA)
 
-  # Outfile --------------------------------------------
-
-  outfile <- cmh_clean %>%
+  cmh_processed <- cmh_clean %>%
     dplyr::select(
       "year",
       "recid",
@@ -73,10 +71,11 @@ process_extract_cmh <- function(data,
     )
 
   if (write_to_disk) {
-    # Save as rds file
-    outfile %>%
-      write_file(get_source_extract_path(year, "CMH", check_mode = "write"))
+    write_file(
+      cmh_processed,
+      get_source_extract_path(year, "CMH", check_mode = "write")
+    )
   }
 
-  return(outfile)
+  return(cmh_processed)
 }

R/process_extract_consultations.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' GP OOH Consultations extract, it will return the final data
-#' but also write this out as an rds.
+#' and (optionally) write it to disk.
 #'
 #' @param data The extract to process
 #' @param year The year to process, in FY format.

R/process_extract_delayed_discharges.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' delayed discharges extract, it will return the final data
-#' but also write this out as an rds.
+#' and (optionally) write it to disk.
 #'
 #' @param data The extract to process
 #' @param year The year to process, in FY format.

R/process_extract_district_nursing.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' District Nursing extract, it will return the final data
-#' but also write this out an rds.
+#' and (optionally) write it to disk.
 #'
 #' @param data The extract to process
 #' @param year The year to process, in FY format.

R/process_extract_gp_ooh.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' GP OoH extract, it will return the final data
-#' but also write this out an rds.
+#' and (optionally) write it to disk.
 #'
 #' @param year The year to process, in FY format.
 #' @param data_list A list containing the extracts.

R/process_extract_home_care.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' (year specific) Home Care extract, it will return the final data
-#' but also write this out as rds.
+#' and (optionally) write it to disk.
 #'
 #' @inheritParams process_extract_care_home
 #'

R/process_extract_homelessness.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' homelessness extract, it will return the final data
-#' and optionally write it out as rds.
+#' and (optionally) write it to disk.
 #'
 #' @param data The extract to process from [read_extract_homelessness()].
 #' @param year The year to process, in FY format.

R/process_extract_maternity.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' maternity extract, it will return the final data
-#' but also write this out an rds.
+#' and (optionally) write it to disk.
 #'
 #' @param data The extract to process
 #' @param year The year to process, in FY format.
@@ -63,10 +63,7 @@ process_extract_maternity <- function(data, year, write_to_disk = TRUE) {
       )
     )
 
-
-  # Save outfile------------------------------------------------
-
-  outfile <- maternity_clean %>%
+  maternity_processed <- maternity_clean %>%
     dplyr::select(
       "year",
       "recid",
@@ -113,12 +110,11 @@ process_extract_maternity <- function(data, year, write_to_disk = TRUE) {
     dplyr::arrange(.data$chi, .data$record_keydate1)
 
   if (write_to_disk) {
-    # Save as rds file
-    outfile %>%
-      write_file(
-        get_source_extract_path(year, "Maternity", check_mode = "write")
-      )
+    write_file(
+      maternity_processed,
+      get_source_extract_path(year, "Maternity", check_mode = "write")
+    )
   }
 
-  return(outfile)
+  return(maternity_processed)
 }

R/process_extract_mental_health.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' mental health extract, it will return the final data
-#' but also write this out an rds.
+#' and (optionally) write it to disk.
 #'
 #' @param data The extract to process
 #' @param year The year to process, in FY format.
@@ -67,10 +67,7 @@ process_extract_mental_health <- function(data, year, write_to_disk = TRUE) {
       smrtype = add_smr_type(.data$recid)
     )
 
-
-  # Outfile  ---------------------------------------
-
-  outfile <- mh_clean %>%
+  mh_processed <- mh_clean %>%
     dplyr::arrange(.data$chi, .data$record_keydate1) %>%
     dplyr::select(
       "year",
@@ -118,10 +115,11 @@ process_extract_mental_health <- function(data, year, write_to_disk = TRUE) {
     )
 
   if (write_to_disk) {
-    outfile %>%
-      # Save as rds file
-      write_file(get_source_extract_path(year, "MH", check_mode = "write"))
+    write_file(
+      mh_processed,
+      get_source_extract_path(year, "MH", check_mode = "write")
+    )
   }
 
-  return(outfile)
+  return(mh_processed)
 }

R/process_extract_ooh_diagnosis.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' GP OOH Diagnosis extract, it will return the final data
-#' but also write this out an rds.
+#' and (optionally) write it to disk.
 #'
 #' @param data The extract to process
 #' @param year The year to process, in FY format.

R/process_extract_ooh_outcomes.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' GP OOH Outcomes extract, it will return the final data
-#' but also write this out as an rds.
+#' and (optionally) write it to disk.
 #'
 #' @param data The extract to process
 #' @param year The year to process, in FY format.

R/process_extract_outpatients.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' outpatients extract, it will return the final data
-#' but also write this out as an rds.
+#' and (optionally) write it to disk.
 #'
 #' @param data The extract to process
 #' @param year The year to process, in FY format.
@@ -49,11 +49,7 @@ process_extract_outpatients <- function(data, year, write_to_disk = TRUE) {
       )
     )
 
-
-  ## save outfile ---------------------------------------
-
-  outfile <-
-    outpatients_clean %>%
+  outpatients_processed <- outpatients_clean %>%
     dplyr::select(
       "year",
       "recid",
@@ -89,12 +85,11 @@ process_extract_outpatients <- function(data, year, write_to_disk = TRUE) {
     )
 
   if (write_to_disk) {
-    # Save as rds file
-    outfile %>%
-      write_file(
-        get_source_extract_path(year, "Outpatients", check_mode = "write")
-      )
+    write_file(
+      outpatients_processed,
+      get_source_extract_path(year, "Outpatients", check_mode = "write")
+    )
   }
 
-  return(outfile)
+  return(outpatients_processed)
 }

R/process_extract_prescribing.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' prescribing extract, it will return the final data
-#' but also write this out as an rds.
+#' and (optionally) write it to disk.
 #'
 #' @param data The extract to process
 #' @param year The year to process, in FY format.
@@ -50,9 +50,10 @@ process_extract_prescribing <- function(data, year, write_to_disk = TRUE) {
   }
 
   if (write_to_disk) {
-    # Save as rds file
-    pis_clean %>%
-      write_file(get_source_extract_path(year, "PIS", check_mode = "write"))
+    write_file(
+      pis_clean,
+      get_source_extract_path(year, "PIS", check_mode = "write")
+    )
   }
 
   return(pis_clean)